The expression platform and the aptamer: cooperativity between Mg2+ and ligand in the SAM-I riboswitch
Abstract
Riboswitch operation involves the complex interplay between the aptamer domain and the expression platform. During transcription, these two domains compete against each other for shared sequence. In this study, we explore the cooperative effects of ligand binding and Magnesium interactions in the SAM-I riboswitch in the context of aptamer collapse and anti-terminator formation. Overall, our studies show the apo-aptamer acts as (i) a pre-organized aptamer competent to bind ligand and undergo structural collapse and (ii) a conformation that is more accessible to anti-terminator formation. We show that both Mg2+ ions and SAM are required for a collapse transition to occur. We then use competition between the aptamer and expression platform for shared sequence to characterize the stability of the collapsed aptamer. We find that SAM and Mg2+ interactions in the aptamer are highly cooperative in maintaining switch polarity (i.e. aptamer ‘off-state’ versus anti-terminator ‘onstate’). We further show that the aptamer off-state is preferentially stabilized by Mg2+ and similar divalent ions. Furthermore, the functional switching assay was used to select for phosphorothioate interference, and identifies potential magnesium chelation sites while characterizing their coordinated role with SAM in aptamer stabilization. In addition, we find that Mg2+ interactions with the apo-aptamer are requiredmore »
- Authors:
-
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- Publication Date:
- Research Org.:
- Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
- OSTI Identifier:
- 1625510
- Grant/Contract Number:
- AC52-06NA25396
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nucleic Acids Research
- Additional Journal Information:
- Journal Volume: 41; Journal Issue: 3; Journal ID: ISSN 0305-1048
- Publisher:
- Oxford University Press
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Biochemistry & Molecular Biology
Citation Formats
Hennelly, Scott P., Novikova, Irina V., and Sanbonmatsu, Karissa Y. The expression platform and the aptamer: cooperativity between Mg2+ and ligand in the SAM-I riboswitch. United States: N. p., 2012.
Web. doi:10.1093/nar/gks978.
Hennelly, Scott P., Novikova, Irina V., & Sanbonmatsu, Karissa Y. The expression platform and the aptamer: cooperativity between Mg2+ and ligand in the SAM-I riboswitch. United States. https://doi.org/10.1093/nar/gks978
Hennelly, Scott P., Novikova, Irina V., and Sanbonmatsu, Karissa Y. Wed .
"The expression platform and the aptamer: cooperativity between Mg2+ and ligand in the SAM-I riboswitch". United States. https://doi.org/10.1093/nar/gks978. https://www.osti.gov/servlets/purl/1625510.
@article{osti_1625510,
title = {The expression platform and the aptamer: cooperativity between Mg2+ and ligand in the SAM-I riboswitch},
author = {Hennelly, Scott P. and Novikova, Irina V. and Sanbonmatsu, Karissa Y.},
abstractNote = {Riboswitch operation involves the complex interplay between the aptamer domain and the expression platform. During transcription, these two domains compete against each other for shared sequence. In this study, we explore the cooperative effects of ligand binding and Magnesium interactions in the SAM-I riboswitch in the context of aptamer collapse and anti-terminator formation. Overall, our studies show the apo-aptamer acts as (i) a pre-organized aptamer competent to bind ligand and undergo structural collapse and (ii) a conformation that is more accessible to anti-terminator formation. We show that both Mg2+ ions and SAM are required for a collapse transition to occur. We then use competition between the aptamer and expression platform for shared sequence to characterize the stability of the collapsed aptamer. We find that SAM and Mg2+ interactions in the aptamer are highly cooperative in maintaining switch polarity (i.e. aptamer ‘off-state’ versus anti-terminator ‘onstate’). We further show that the aptamer off-state is preferentially stabilized by Mg2+ and similar divalent ions. Furthermore, the functional switching assay was used to select for phosphorothioate interference, and identifies potential magnesium chelation sites while characterizing their coordinated role with SAM in aptamer stabilization. In addition, we find that Mg2+ interactions with the apo-aptamer are required for the full formation of the anti-terminator structure, and that higher concentrations of Mg2+ (>4 mM) shift the equilibrium toward the anti-terminator on-state even in the presence of SAM.},
doi = {10.1093/nar/gks978},
journal = {Nucleic Acids Research},
number = 3,
volume = 41,
place = {United States},
year = {Wed Dec 19 00:00:00 EST 2012},
month = {Wed Dec 19 00:00:00 EST 2012}
}
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